InĀ [1]:
"""
variables:
1) folder: The directory containing the input topology and the trajectory files.
2) topology_file
3) trajectory_file
4) all-residue samples' output_dir
5) 2-residue samples' output_dir, (to focus on in-conformation and out-conformation)
do I need all five here? yes
"""
"""
when I run visualize_mda_universe, it creates 190 odd samples;
the samples are used by pymol under the wraps, for visualization
"""
from visualize import visualize_mda_universe # local file
import os
"""
folder = "/home/uni/capstone/test-bioemu-ubq/"
topology_file = os.path.join(folder, "topology.pdb")
trajectory_file = os.path.join(folder, "samples.xtc")
"""
"""
folder = "/home/uni/capstone/2k39_7686d/hpacker-openmm/"
topology_file = os.path.join(folder, "hpacker-openmm-md-equil.pdb")
trajectory_file = os.path.join(folder, "hpacker-openmm-md-equil.xtc")
"""
"""
folder = "/home/uni/capstone/2k39_7686d/hpacker-openmm/"
os.path.join(folder, "hpacker-openmm_sidechain_rec.pdb")
topology_file = os.path.join(folder, "hpacker-openmm_sidechain_rec.pdb")
trajectory_file = os.path.join(folder, "hpacker-openmm_sidechain_rec.xtc")
"""
"""
folder = "/home/uni/bioemu-project/samples/"
topology_file = os.path.join(folder, "topology.pdb")
trajectory_file = os.path.join(folder, "samples.xtc")
"""
"""
folder = "/home/uni/necessary-things-for-recreating-bioemu-project-from-scratch/"
topology_file = os.path.join(folder, ".2k39-backbone-bioemu-samples/topology.pdb")
trajectory_file = os.path.join(folder, ".2k39-backbone-bioemu-samples/samples.xtc")
"""
"""
folder = "/home/uni/necessary-things-for-recreating-bioemu-project-from-scratch/"
topology_file = os.path.join(folder, "2k39-backbone-bioemu-samples/topology.pdb")
trajectory_file = os.path.join(folder, "visualization-fixed/combined-samples-trajectory.pdb")
"""
folder = "/home/uni/necessary-things-for-recreating-bioemu-project-from-scratch/"
topology_file = os.path.join(folder, "PDBs/topology-1200-odd-atoms.pdb")
trajectory_file = os.path.join(folder, "PDBs/visualization-1200-odd-atoms/combined-samples-trajectory.pdb")
import MDAnalysis as mda
u = mda.Universe(topology_file, trajectory_file)
view = visualize_mda_universe(u,
output_dir="/home/uni/necessary-things-for-recreating-bioemu-project-from-scratch/PDBs/visualization-1200-odd-atoms-and-ran-through-pipeline",)
view.show()
/home/uni/miniconda3/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm
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